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MicroRNAs are regulators in regulation of broad range of phenotypes. The purple urchin, Strongylocentrotus nudus, is one of the most important marine economic animals that widely distributed in the cold seas along the coasts of eastern pacific area. To date, only 45 microRNAs have been identified in a related species, Strongylocentrotus purpurtus, and there is no report on S. nudus microRNAs. Herein, solexa sequencing technology was used to high throughput sequencing analysis of microRNAs in small RNA library isolated from five tissues of S. nudus. Totally, 8,966,865 reads were yielded, 131,015 of which were related to 415 unique microRNAs including 345 deuterostoma conserved and 70 urchin specific microRNAs, as well as 5 microRNA* sequences. The miRNA features including length distribution, end variations and genomic locations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways that regulated by urchin miRNAs, of which signal transduction mechanisms was the subgroup containing the maximum targets. In addition, the expression of 100 miRNAs in female gonad was confirmed using microRNA microarray analysis. This study provides a first large scale cloning and characterization of S.nudus miRNAs and their potential targets, providing the foundation for further characterization for their role in the regulation of diversity of physiological processes.

Bacterial community plays an important role in keeping the health status of the host. A study on the characteristics of gut bacterial community of sea cucumber (Apostichopus japonicus) not only helps improve the current aquaculture model, but promotes healthy and rapid development of the aquaculture industry as well. Therefore, taking pond‐cultured sea cucumber (A. japonicus) as the studying object, the metagenomic and 16S rRNA sequencing technology were used in this study to explore the characteristics of bacterial community in different parts of the gut of sea cucumber, as well as during gut regeneration after evisceration. The results showed that the compositions of bacterial community are different in varying parts of the gut of sea cucumber (A. japonicus). Specifically, bacterial community in the midgut and hindgut are highly similar, showing significantly diversified bacterial species compared to the foregut. GO annotation indicated that the foregut is associated with richer catalytic activity and binding than the midgut and the hindgut. According to the KEGG annotation, metabolism‐related genes are mainly concentrated in the foregut, while genes related to signal transduction and the immune system are mostly annotated in the midgut and hindgut. During the gut regeneration stage, the structure of bacterial community varied greatly in different stage of the regeneration stage, with significant differences between the earlier and later stage. The dominant bacteria in the earlier stage is Rubritalea, and that in the later stage is Arcobacter. Besides, there were Loktanella, Thalassobacter and Phaeobacter in the gut throughout the entire regeneration stage. Cupriavidus, Hellea, HTCC2207, Methylophaga, Methylotenera, Stenotrophomonas and Tenacibaculum were only present in the earlier stage, and gradually disappeared in the later stage due to improving gut functions. The abundance and diversity of bacteria in the gut were higher in the earlier regeneration stage than that in the later stage, with a peak between the 15th and 25th day of the regeneration stage. At 45th day, the abundance and diversity became stable.

No abstract

This study investigated the genetic variation and genotype-environment interaction (GEI) in the early growth stage among seven full-sib families of the sea urchin Strongylocentrotus intermedius. From each of the seven families, 180 or 270 sea urchins of the same size were exposed to three laboratory environments (E 1 , E 2 and E 3 ). These environments were commonly used in breeding programs for S. intermedius. After a 102 days trial, test height, test diameter, body weight and the coefficient of variation of body weight were determined. The results revealed significant family effects on most growth traits in all the three environments (except for test diameter in environment E 2 ), and significant environmental effects on growth in several families (family 1, 5, 6, 7). The study also revealed that the coefficient of variation in body weight varied significantly among the families (P < 0.01) but not among the environments. Highly significant GEI effects were also recorded for all growth traits (P 0.001), except for the coefficient of variation in body weight (P > 0.05). Variances of GEI accounted for about 0-2.742% of phenotypic variances for the investigated traits. Significant GEI caused a certain degree family ranking inversions for the growth traits. The present study provides evidence for the existence of GEI in the family selection of sea urchin S. intermedius. More attention should be paid to the GEI to obtain satisfactory genetic gain in S. intermedius.

To explore the impact of chronic heat stress on commercial echinoderms, the present study assessed the effects of chronic high temperature on the growth, survival, feeding, and differential gene expression in the sea urchin Strongylocentrotus intermedius cultured in northern Yellow Sea in China. One suitable seawater condition (20°C) and one laboratory-controlled high temperature condition (25°C) were set up. After 28 days incubation, our results showed that: (1) The specific growth, survival, and ingestion rates of S. intermedius reared under high temperature (25°C) decreased compared to those reared under optimal temperature (20°C) conditions; (2) comparative transcriptome analysis identified 2,125 differentially expressed genes (DEGs) in S. intermedius reared under high temperature (25°C) compared to those subjected to optimal temperature condition (20°C), which included 1,015 upregulated and 1,100 downregulated genes. The accuracy of the transcriptome profiles was verified by quantitative real-time PCR (qRT-PCR). Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that these DEGs mainly enriched the functional categories of ribosome, protein processing in endoplasmic reticulum, and prion diseases. A total of 732 temperature-induced expressed genes, such as ATP5, heat shock protein 70, and heat shock protein 90, were identified as candidates that were closely correlated with heat resistance in S. intermedius . Differentially expressed transcription factors (TFs), such as AP-1, Fos, CREB, and ZNF, were also identified as potential regulators that regulate the molecular network that was associated with responses to heat stress in sea urchins. Observations in the present study provide additional information that improves our understanding of the molecular mechanism of temperate echinoid species in response to heat stress, as well as theoretical basis for the molecular-assisted breeding of heat-resistant sea urchins.

No abstract

The purpose of the present study was to develop in silico models allowing for a reliable prediction of androgenic and nonandrogenic compounds based on a large diverse dataset of 205 compounds. As a new classification method, the Random Forest (RF) was applied, its performance to classify these compounds in terms of their Quantitative Structure -Activity Relationships (QSAR) was evaluated and also compared with the widely used Partial Least Squares (PLS) analysis for the dataset. The predictive power of these methods was verified with five-fold cross-validation and an independent test set. For the RF model, the prediction accuracies of the androgenic and nonandrogenic compounds are 81.0 and 77.0% for cross-validation, respectively, averaging 87.3% of correctly classified compounds in the external tests. The PLS is slightly weak, showing an average prediction accuracy of 75 and 74.7% for the cross-validation and external validation, respectively. Our analysis demonstrates that RF is a powerful tool capable of building models for the data and should be valuable for virtual screening of androgen receptor-binding ligands.